The skimmer has been running for four months now, so break-in isn't a problem. Coralvue's website is awful, and it is completely unclear what depth the water should be, but the website used to say 5.5" previously. If you read the directions with the skimmer, they actually say the output of the gate valve should be above the water level, which is impossible with this skimmer. Their manuals are terrible.
Regardless, I will try to raise the water level as some of you suggested and see what that does. Thanks guys.